They both can use in the context. I prefer #2.
We use '' i am doing'' (present continuous) when we say what we have arranged to do, but if we use '' i am going to do something'' we say that we have decided to do it (but perhaps not arranged to do it), so i think in this situation ''I am seeing the dentist tomorrow at 3'' seems to be more proper.
and also i reject 'I see the dentist tomorrow at 3' because we use simple present to talk about things in general, but I'm not sure about 'I will see the dentist tomorrow at 3'!so
I'd use more than one!!!